FIELDimageR pipeline:
Phenomics applied to plant breeding

Introduction

Agriculture and plant breeding

Images can be used in plant phenotyping to draw inference about many traits:

  • Geometric traits (i.e. plant height, leaf area index, lodging, crop canopy cover)
  • Canopy spectral texture (spectral features)
  • Physiological traits (i.e., chlorophyll, biomass, pigment content, photosynthesis)
  • Abiotic/biotic stress indicators (i.e., stomatal conductance, canopy temperature difference, leaf water potential, senescence index)
  • Nutrients (nitrogen concentration, protein content)
  • Yield


FIELDimageR

FIELDimageR is a R package to analyze images and plant phenotyping, and allows to:

  • Crop the image
  • Remove soil effect
  • Build vegetation indices
  • Rotate the image
  • Build the plot shapefile
  • Extract information for each plot
  • Evaluate stand count, canopy percentage, and plant height


FIELDimageR pipeline

1) Example 01

Remote sensing - RGB and DSM - (Potato Breeding)

Jeffrey Endelman and Filipe Matias (UW-Madison)

Data (R/FIELDimageR)

  • Potato breeding: 140 plots (3x15 feet)
  • Population: 97 genotypes
  • Six UAV flights: 30 (soil base), 40, 70, and 100 days after planting (DAP)

  • Download EX1: RGB orthomosaics.tif MOSAIC and dsm.tif DSM

Estimation of plant height using digital surface model (DSM).

Evaluating all mosaics in a loop

  • Graphics

  • Linear Regression

  • Heritability

2) Example 02

Hyperspectral (Potato Breeding)

Jeffrey Endelman and Filipe Matias (UW-Madison)

Data Info (R/FIELDimageR)

  • Potato breeding: 196 plots (3x15 feet)
  • Population: 138 genotypes
  • HTP Platform (Dr. Philip Townsend UM-Madison): Cessna-180 airplane + HySpex VNIR-1800 + HySpex SWIR-384
  • Hyperspectral Data: 474 bands

Making the mask by using the RGB to calculate vegetation indices and to remove the soil



Reference

Matias, F.I. (2019). FIELDimageR Pipeline (tutorial). https://github.com/filipematias23/FIELDimageR

Matias, F.I.; Caraza-Harter, M.; Endelman, J.B. (2020). FIELDimageR: A R Package to Analyze Orthomosaic Images from Agricultural Field Trials. The Plant Phenome Journal. DOI:10.1002/ppj2.20005

Filipe Matias
Department of Horticulture
University of Wisconsin-Madison

2021-04-07